Summary

Tag	sgn_unigenes
Owner	SGN
Input	contig or BAC sequences
Output	GenomeThreader alignments of SGN unigenes to the genome
Depends	seq

Aligns current set of all SGN unigenes to the genome. Runs GenomeThreader as

          'gth',
          '-gff3out',
          '-intermediate',
          '-force',
          -autointroncutout  => 200,
          '-gcmaxgapwidth'   => 25000, #< max gap in any alignment, this is 1.2x the largest intron size we have seen so far
          -minalignmentscore => '0.90',
          -mincoverage       => '0.90',
          -seedlength        => 16,
          -o                 => "$temp_gff3",
          -species           => 'arabidopsis',
          -cdna              => "$temp_cdna",
          -genomic           => $un_xed_seqs,

Input

un-Xed contig/BAC sequence from seq analysis (AnSgnChecks000)

Requirements

genomic sequences, no X masking, fasta format

Processing

Runs GenomeThreader as gth -xmlout -minalignmentscore 0.90 -mincoverage 0.90 -seedlength 16 -species arabidopsis -cdna sgn_unigenes.fasta -genomic <contig/bac seq>

Output

GenomeThreader XML, GFF3 representation of the GenomeThreader results

Filenames

gth:xml, unigenes:gff3

Requirements

valid gthxml, valid GFF3

CategoryAnalysisDescription CategoryAnSgnUnigenes